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Structure of Agrobacterium tumefaciens VirB8 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BHM PDB ENTRY 2BHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.1 M SODIUM ACETATE, PH 4.6, 0.2 M SODIUM BROMIDE, 20% MPD
Crystal Properties Matthews coefficient Solvent content 2.68 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.269 α = 90 b = 72.349 β = 110.66 c = 48.844 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2004-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 50 96.3 0.13 12.4 5.2 17972
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 88.6 0.29 4.3 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BHM 2.2 20 17010 928 96.1 0.239 0.235 0.2336 0.301 0.2983 RANDOM 16.68
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.82 0.33 -0.25 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.817 r_dihedral_angle_3_deg 20.255 r_dihedral_angle_4_deg 18.217 r_dihedral_angle_1_deg 6.497 r_scangle_it 4.248 r_mcangle_it 3.727 r_scbond_it 2.952 r_mcbond_it 2.59 r_angle_refined_deg 1.61 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.817 r_dihedral_angle_3_deg 20.255 r_dihedral_angle_4_deg 18.217 r_dihedral_angle_1_deg 6.497 r_scangle_it 4.248 r_mcangle_it 3.727 r_scbond_it 2.952 r_mcbond_it 2.59 r_angle_refined_deg 1.61 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.214 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2290 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing